Natural language recommendation system: to pre-classify inputs or not?
Likely yes!  When you split out the inputs like this, you are adding information.  How much this helps is an open question till you build your system, get some data and start training.  

Of course, it would be marvelous to have a machine do all the work straight unstructured text - but you want a functional, easy-to-use website, not a research project of your own.  To that end, do everything that you can to constrain the scope of the problem, and maximize the information available to your model.  For example, you might want to see if you can add researchers using Google Scholar (so you can link to their profiles, and perhaps mine some information that way).  

You'll be somewhat 'data constrained' till you've got a decent number of research proposals and user interactions to learn from.  Tools like our NLP architect may help you get more out of your text (there are some other really cool new-generation ML-for-NLP packages you should also evaluate).